Multiple sequence alignment - TraesCS6A01G170700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G170700 chr6A 100.000 4293 0 0 1 4293 181507546 181511838 0.000000e+00 7928.0
1 TraesCS6A01G170700 chr6A 95.918 49 2 0 1597 1645 181508957 181509005 3.560000e-11 80.5
2 TraesCS6A01G170700 chr6A 95.918 49 2 0 1412 1460 181509142 181509190 3.560000e-11 80.5
3 TraesCS6A01G170700 chr6D 93.299 2731 132 26 1597 4293 138895522 138898235 0.000000e+00 3982.0
4 TraesCS6A01G170700 chr6D 91.232 1631 79 31 1 1586 138894095 138895706 0.000000e+00 2161.0
5 TraesCS6A01G170700 chr6B 92.414 1806 102 17 1597 3375 238155016 238156813 0.000000e+00 2543.0
6 TraesCS6A01G170700 chr6B 92.815 1517 54 18 103 1594 238153734 238155220 0.000000e+00 2146.0
7 TraesCS6A01G170700 chr6B 96.067 356 12 2 3372 3726 238156894 238157248 2.880000e-161 579.0
8 TraesCS6A01G170700 chr6B 95.389 347 15 1 3713 4058 238157270 238157616 6.270000e-153 551.0
9 TraesCS6A01G170700 chr6B 92.827 237 16 1 4057 4293 238157737 238157972 4.110000e-90 342.0
10 TraesCS6A01G170700 chr6B 95.455 66 3 0 1 66 238153673 238153738 5.870000e-19 106.0
11 TraesCS6A01G170700 chr1A 95.918 49 2 0 4208 4256 471264665 471264617 3.560000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G170700 chr6A 181507546 181511838 4292 False 2696.333333 7928 97.278667 1 4293 3 chr6A.!!$F1 4292
1 TraesCS6A01G170700 chr6D 138894095 138898235 4140 False 3071.500000 3982 92.265500 1 4293 2 chr6D.!!$F1 4292
2 TraesCS6A01G170700 chr6B 238153673 238157972 4299 False 1044.500000 2543 94.161167 1 4293 6 chr6B.!!$F1 4292

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
330 334 0.526662 TTTCTTCGTCTCCGCTCTCC 59.473 55.0 0.00 0.0 0.00 3.71 F
1359 1395 0.033208 GTCAATGGGGGAGGATTGCA 60.033 55.0 0.00 0.0 30.89 4.08 F
1630 1700 0.038159 CCTGTGACACGACCCTTCTC 60.038 60.0 0.22 0.0 0.00 2.87 F
2128 2208 0.187361 TCTTTGAGGGGTGGTTTGGG 59.813 55.0 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1681 0.038159 GAGAAGGGTCGTGTCACAGG 60.038 60.0 3.42 0.0 0.00 4.00 R
3084 3164 0.539438 ACAAACATCGGGGCACACAT 60.539 50.0 0.00 0.0 0.00 3.21 R
3091 3171 0.601057 GAAACCCACAAACATCGGGG 59.399 55.0 0.00 0.0 44.96 5.73 R
3761 3971 0.249868 TGTGGCCACAAGAGAAGACG 60.250 55.0 36.10 0.0 38.56 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.544246 GCAACCGGCCAAAGACTAAAT 59.456 47.619 0.00 0.00 36.11 1.40
35 36 5.258051 ACCGGCCAAAGACTAAATTAATCA 58.742 37.500 0.00 0.00 0.00 2.57
232 233 2.475111 ACGCGGCATTCGTCAATATAAG 59.525 45.455 12.47 0.00 41.72 1.73
276 277 1.201880 GAGGGACAACTCCGTCTACAC 59.798 57.143 2.79 0.00 44.88 2.90
277 278 0.963962 GGGACAACTCCGTCTACACA 59.036 55.000 0.00 0.00 37.46 3.72
278 279 1.342174 GGGACAACTCCGTCTACACAA 59.658 52.381 0.00 0.00 37.46 3.33
279 280 2.609737 GGGACAACTCCGTCTACACAAG 60.610 54.545 0.00 0.00 37.46 3.16
330 334 0.526662 TTTCTTCGTCTCCGCTCTCC 59.473 55.000 0.00 0.00 0.00 3.71
482 486 3.276857 CCATTCCAGTTGTCTGATCTGG 58.723 50.000 15.44 15.44 46.94 3.86
492 496 7.202001 CCAGTTGTCTGATCTGGTTGGTATATA 60.202 40.741 14.16 0.00 43.76 0.86
521 525 3.897505 AGAAGTTTGTCTTGGATTTGGGG 59.102 43.478 0.00 0.00 36.40 4.96
572 576 5.049060 TGAATGTTTGTCCATTCTTGTACCG 60.049 40.000 13.28 0.00 47.00 4.02
640 648 2.665519 CGGAAATGGCACTCGAAGTTTG 60.666 50.000 0.00 0.00 0.00 2.93
666 674 4.261447 GCTTTATGTGGTTTCGTTTCCTGT 60.261 41.667 0.00 0.00 0.00 4.00
699 708 3.557054 GCCAGACTTTGTACATCCTGTCA 60.557 47.826 15.40 0.00 0.00 3.58
702 711 5.707298 CCAGACTTTGTACATCCTGTCAAAT 59.293 40.000 15.40 0.00 31.89 2.32
708 717 3.993736 TGTACATCCTGTCAAATGTGTCG 59.006 43.478 9.68 0.00 36.78 4.35
971 1007 6.640499 TCTTGTCCTAATTGAAAATTTGCACG 59.360 34.615 0.00 0.00 0.00 5.34
1051 1087 0.947244 CCAGTCTGCACACAAGGAAC 59.053 55.000 0.00 0.00 0.00 3.62
1323 1359 3.262915 AGATTACATCCTATGGCTGGCTC 59.737 47.826 2.00 0.00 33.60 4.70
1359 1395 0.033208 GTCAATGGGGGAGGATTGCA 60.033 55.000 0.00 0.00 30.89 4.08
1387 1423 3.436704 AGCATCTGTGGTCATAAACAACG 59.563 43.478 0.00 0.00 34.15 4.10
1501 1568 7.170998 GCAGTATACGTTCAGGTGCTATATTTT 59.829 37.037 0.00 0.00 0.00 1.82
1506 1573 7.535489 ACGTTCAGGTGCTATATTTTTAGTC 57.465 36.000 0.00 0.00 0.00 2.59
1507 1574 6.537660 ACGTTCAGGTGCTATATTTTTAGTCC 59.462 38.462 0.00 0.00 0.00 3.85
1508 1575 6.537301 CGTTCAGGTGCTATATTTTTAGTCCA 59.463 38.462 0.00 0.00 0.00 4.02
1512 1579 8.439971 TCAGGTGCTATATTTTTAGTCCATGAT 58.560 33.333 0.00 0.00 0.00 2.45
1531 1598 7.621285 TCCATGATTTACATAAAATGGAACCCA 59.379 33.333 12.42 0.00 38.58 4.51
1537 1604 7.798710 TTACATAAAATGGAACCCATGGAAA 57.201 32.000 15.22 0.00 44.40 3.13
1552 1622 8.803397 ACCCATGGAAACTAAGTAATAACTTC 57.197 34.615 15.22 0.00 42.42 3.01
1554 1624 9.462606 CCCATGGAAACTAAGTAATAACTTCTT 57.537 33.333 15.22 0.00 42.42 2.52
1592 1662 5.883661 AGTGAATGCTGATACATTTTTCGG 58.116 37.500 0.00 0.00 40.31 4.30
1593 1663 5.415701 AGTGAATGCTGATACATTTTTCGGT 59.584 36.000 0.00 0.00 40.31 4.69
1594 1664 5.512788 GTGAATGCTGATACATTTTTCGGTG 59.487 40.000 0.00 0.00 40.31 4.94
1595 1665 5.414144 TGAATGCTGATACATTTTTCGGTGA 59.586 36.000 0.00 0.00 40.31 4.02
1596 1666 5.895636 ATGCTGATACATTTTTCGGTGAA 57.104 34.783 0.00 0.00 0.00 3.18
1597 1667 5.895636 TGCTGATACATTTTTCGGTGAAT 57.104 34.783 0.00 0.00 0.00 2.57
1598 1668 6.266168 TGCTGATACATTTTTCGGTGAATT 57.734 33.333 0.00 0.00 0.00 2.17
1599 1669 7.384439 TGCTGATACATTTTTCGGTGAATTA 57.616 32.000 0.00 0.00 0.00 1.40
1600 1670 7.995289 TGCTGATACATTTTTCGGTGAATTAT 58.005 30.769 0.00 0.00 0.00 1.28
1601 1671 8.128582 TGCTGATACATTTTTCGGTGAATTATC 58.871 33.333 0.00 0.00 0.00 1.75
1602 1672 8.128582 GCTGATACATTTTTCGGTGAATTATCA 58.871 33.333 0.00 0.00 0.00 2.15
1612 1682 4.946784 GGTGAATTATCATCGGTATGCC 57.053 45.455 0.00 0.00 38.01 4.40
1613 1683 4.579869 GGTGAATTATCATCGGTATGCCT 58.420 43.478 0.00 0.00 38.01 4.75
1614 1684 4.393062 GGTGAATTATCATCGGTATGCCTG 59.607 45.833 0.00 0.00 38.01 4.85
1615 1685 4.997395 GTGAATTATCATCGGTATGCCTGT 59.003 41.667 0.00 0.00 38.01 4.00
1616 1686 4.996758 TGAATTATCATCGGTATGCCTGTG 59.003 41.667 0.00 0.00 32.76 3.66
1617 1687 4.890158 ATTATCATCGGTATGCCTGTGA 57.110 40.909 0.00 2.44 32.76 3.58
1618 1688 2.533266 ATCATCGGTATGCCTGTGAC 57.467 50.000 6.25 0.00 31.69 3.67
1619 1689 1.190643 TCATCGGTATGCCTGTGACA 58.809 50.000 0.00 0.00 32.76 3.58
1620 1690 1.134818 TCATCGGTATGCCTGTGACAC 60.135 52.381 0.00 0.00 32.76 3.67
1621 1691 0.179111 ATCGGTATGCCTGTGACACG 60.179 55.000 0.22 0.00 0.00 4.49
1622 1692 1.214325 CGGTATGCCTGTGACACGA 59.786 57.895 0.22 0.00 0.00 4.35
1623 1693 1.076533 CGGTATGCCTGTGACACGAC 61.077 60.000 0.22 0.00 0.00 4.34
1624 1694 0.739813 GGTATGCCTGTGACACGACC 60.740 60.000 0.22 0.00 0.00 4.79
1625 1695 0.739813 GTATGCCTGTGACACGACCC 60.740 60.000 0.22 0.00 0.00 4.46
1626 1696 0.902984 TATGCCTGTGACACGACCCT 60.903 55.000 0.22 0.00 0.00 4.34
1627 1697 1.768684 ATGCCTGTGACACGACCCTT 61.769 55.000 0.22 0.00 0.00 3.95
1628 1698 1.668151 GCCTGTGACACGACCCTTC 60.668 63.158 0.22 0.00 0.00 3.46
1629 1699 2.050269 CCTGTGACACGACCCTTCT 58.950 57.895 0.22 0.00 0.00 2.85
1630 1700 0.038159 CCTGTGACACGACCCTTCTC 60.038 60.000 0.22 0.00 0.00 2.87
1631 1701 0.962489 CTGTGACACGACCCTTCTCT 59.038 55.000 0.22 0.00 0.00 3.10
1632 1702 0.673985 TGTGACACGACCCTTCTCTG 59.326 55.000 0.22 0.00 0.00 3.35
1633 1703 0.674534 GTGACACGACCCTTCTCTGT 59.325 55.000 0.00 0.00 0.00 3.41
1634 1704 0.959553 TGACACGACCCTTCTCTGTC 59.040 55.000 0.00 0.00 33.30 3.51
1635 1705 0.959553 GACACGACCCTTCTCTGTCA 59.040 55.000 0.00 0.00 32.99 3.58
1636 1706 1.546476 GACACGACCCTTCTCTGTCAT 59.454 52.381 0.00 0.00 32.99 3.06
1637 1707 1.273606 ACACGACCCTTCTCTGTCATG 59.726 52.381 0.00 0.00 31.44 3.07
1638 1708 0.247736 ACGACCCTTCTCTGTCATGC 59.752 55.000 0.00 0.00 0.00 4.06
1639 1709 0.460987 CGACCCTTCTCTGTCATGCC 60.461 60.000 0.00 0.00 0.00 4.40
1640 1710 0.908198 GACCCTTCTCTGTCATGCCT 59.092 55.000 0.00 0.00 0.00 4.75
1641 1711 2.111384 GACCCTTCTCTGTCATGCCTA 58.889 52.381 0.00 0.00 0.00 3.93
1642 1712 1.834263 ACCCTTCTCTGTCATGCCTAC 59.166 52.381 0.00 0.00 0.00 3.18
1643 1713 2.114616 CCCTTCTCTGTCATGCCTACT 58.885 52.381 0.00 0.00 0.00 2.57
1644 1714 2.503356 CCCTTCTCTGTCATGCCTACTT 59.497 50.000 0.00 0.00 0.00 2.24
1645 1715 3.706594 CCCTTCTCTGTCATGCCTACTTA 59.293 47.826 0.00 0.00 0.00 2.24
1646 1716 4.442192 CCCTTCTCTGTCATGCCTACTTAC 60.442 50.000 0.00 0.00 0.00 2.34
1647 1717 4.442192 CCTTCTCTGTCATGCCTACTTACC 60.442 50.000 0.00 0.00 0.00 2.85
1648 1718 3.708451 TCTCTGTCATGCCTACTTACCA 58.292 45.455 0.00 0.00 0.00 3.25
1649 1719 4.290093 TCTCTGTCATGCCTACTTACCAT 58.710 43.478 0.00 0.00 0.00 3.55
1650 1720 4.342378 TCTCTGTCATGCCTACTTACCATC 59.658 45.833 0.00 0.00 0.00 3.51
1651 1721 3.068165 TCTGTCATGCCTACTTACCATCG 59.932 47.826 0.00 0.00 0.00 3.84
1652 1722 3.028130 TGTCATGCCTACTTACCATCGA 58.972 45.455 0.00 0.00 0.00 3.59
1653 1723 3.068165 TGTCATGCCTACTTACCATCGAG 59.932 47.826 0.00 0.00 0.00 4.04
1654 1724 3.318275 GTCATGCCTACTTACCATCGAGA 59.682 47.826 0.00 0.00 0.00 4.04
1655 1725 3.570125 TCATGCCTACTTACCATCGAGAG 59.430 47.826 0.00 0.00 0.00 3.20
1656 1726 3.014304 TGCCTACTTACCATCGAGAGT 57.986 47.619 0.00 0.00 0.00 3.24
1657 1727 3.362706 TGCCTACTTACCATCGAGAGTT 58.637 45.455 0.00 0.00 0.00 3.01
1658 1728 3.130516 TGCCTACTTACCATCGAGAGTTG 59.869 47.826 0.00 0.00 0.00 3.16
1659 1729 3.130693 GCCTACTTACCATCGAGAGTTGT 59.869 47.826 0.00 0.00 0.00 3.32
1660 1730 4.337555 GCCTACTTACCATCGAGAGTTGTA 59.662 45.833 0.00 0.00 0.00 2.41
1661 1731 5.163581 GCCTACTTACCATCGAGAGTTGTAA 60.164 44.000 0.00 0.00 0.00 2.41
1662 1732 6.461231 GCCTACTTACCATCGAGAGTTGTAAT 60.461 42.308 0.00 0.00 0.00 1.89
1663 1733 6.918569 CCTACTTACCATCGAGAGTTGTAATG 59.081 42.308 0.00 0.00 0.00 1.90
1664 1734 6.282199 ACTTACCATCGAGAGTTGTAATGT 57.718 37.500 0.00 0.00 0.00 2.71
1665 1735 6.698380 ACTTACCATCGAGAGTTGTAATGTT 58.302 36.000 0.00 0.00 0.00 2.71
1666 1736 6.590292 ACTTACCATCGAGAGTTGTAATGTTG 59.410 38.462 0.00 0.00 0.00 3.33
1667 1737 5.147330 ACCATCGAGAGTTGTAATGTTGA 57.853 39.130 0.00 0.00 0.00 3.18
1668 1738 5.547465 ACCATCGAGAGTTGTAATGTTGAA 58.453 37.500 0.00 0.00 0.00 2.69
1669 1739 6.173339 ACCATCGAGAGTTGTAATGTTGAAT 58.827 36.000 0.00 0.00 0.00 2.57
1670 1740 7.327975 ACCATCGAGAGTTGTAATGTTGAATA 58.672 34.615 0.00 0.00 0.00 1.75
1671 1741 7.987458 ACCATCGAGAGTTGTAATGTTGAATAT 59.013 33.333 0.00 0.00 0.00 1.28
1672 1742 8.491152 CCATCGAGAGTTGTAATGTTGAATATC 58.509 37.037 0.00 0.00 0.00 1.63
1673 1743 7.679659 TCGAGAGTTGTAATGTTGAATATCG 57.320 36.000 0.00 0.00 0.00 2.92
1674 1744 7.477494 TCGAGAGTTGTAATGTTGAATATCGA 58.523 34.615 0.00 0.00 0.00 3.59
1675 1745 8.135529 TCGAGAGTTGTAATGTTGAATATCGAT 58.864 33.333 2.16 2.16 0.00 3.59
1676 1746 9.394477 CGAGAGTTGTAATGTTGAATATCGATA 57.606 33.333 7.75 7.75 0.00 2.92
1682 1752 9.891828 TTGTAATGTTGAATATCGATAATTGGC 57.108 29.630 9.61 1.44 0.00 4.52
1683 1753 9.283768 TGTAATGTTGAATATCGATAATTGGCT 57.716 29.630 9.61 0.00 0.00 4.75
1684 1754 9.546909 GTAATGTTGAATATCGATAATTGGCTG 57.453 33.333 9.61 0.00 0.00 4.85
1685 1755 7.750229 ATGTTGAATATCGATAATTGGCTGT 57.250 32.000 9.61 0.00 0.00 4.40
1686 1756 8.846943 ATGTTGAATATCGATAATTGGCTGTA 57.153 30.769 9.61 0.00 0.00 2.74
1687 1757 8.846943 TGTTGAATATCGATAATTGGCTGTAT 57.153 30.769 9.61 0.00 0.00 2.29
1688 1758 9.936759 TGTTGAATATCGATAATTGGCTGTATA 57.063 29.630 9.61 0.00 0.00 1.47
1690 1760 8.628882 TGAATATCGATAATTGGCTGTATACG 57.371 34.615 9.61 0.00 0.00 3.06
1691 1761 8.248253 TGAATATCGATAATTGGCTGTATACGT 58.752 33.333 9.61 0.00 0.00 3.57
1692 1762 8.997621 AATATCGATAATTGGCTGTATACGTT 57.002 30.769 9.61 0.00 0.00 3.99
1693 1763 6.946229 ATCGATAATTGGCTGTATACGTTC 57.054 37.500 0.00 0.00 0.00 3.95
1694 1764 5.834169 TCGATAATTGGCTGTATACGTTCA 58.166 37.500 0.00 0.00 0.00 3.18
1695 1765 5.918576 TCGATAATTGGCTGTATACGTTCAG 59.081 40.000 0.00 1.76 35.12 3.02
1696 1766 5.918576 CGATAATTGGCTGTATACGTTCAGA 59.081 40.000 15.66 0.00 34.02 3.27
1697 1767 6.586463 CGATAATTGGCTGTATACGTTCAGAT 59.414 38.462 15.66 0.00 34.02 2.90
1698 1768 5.991328 AATTGGCTGTATACGTTCAGATG 57.009 39.130 15.66 0.00 34.02 2.90
1699 1769 2.821546 TGGCTGTATACGTTCAGATGC 58.178 47.619 15.66 5.30 34.02 3.91
1700 1770 2.430694 TGGCTGTATACGTTCAGATGCT 59.569 45.455 15.66 0.00 34.02 3.79
1701 1771 3.634910 TGGCTGTATACGTTCAGATGCTA 59.365 43.478 15.66 1.47 34.02 3.49
1702 1772 4.280929 TGGCTGTATACGTTCAGATGCTAT 59.719 41.667 15.66 0.00 34.02 2.97
1703 1773 5.475564 TGGCTGTATACGTTCAGATGCTATA 59.524 40.000 15.66 0.00 34.02 1.31
1704 1774 5.800941 GGCTGTATACGTTCAGATGCTATAC 59.199 44.000 15.66 6.00 34.02 1.47
1705 1775 6.349445 GGCTGTATACGTTCAGATGCTATACT 60.349 42.308 15.66 0.00 34.02 2.12
1706 1776 7.085116 GCTGTATACGTTCAGATGCTATACTT 58.915 38.462 15.66 0.00 34.02 2.24
1707 1777 7.595502 GCTGTATACGTTCAGATGCTATACTTT 59.404 37.037 15.66 0.00 34.02 2.66
1708 1778 9.464714 CTGTATACGTTCAGATGCTATACTTTT 57.535 33.333 0.00 0.00 34.02 2.27
1712 1782 7.988904 ACGTTCAGATGCTATACTTTTAGTC 57.011 36.000 0.00 0.00 0.00 2.59
1713 1783 6.691818 ACGTTCAGATGCTATACTTTTAGTCG 59.308 38.462 0.00 0.00 0.00 4.18
1714 1784 6.345093 CGTTCAGATGCTATACTTTTAGTCGC 60.345 42.308 0.00 0.00 0.00 5.19
1715 1785 6.392625 TCAGATGCTATACTTTTAGTCGCT 57.607 37.500 0.00 0.00 0.00 4.93
1716 1786 6.209361 TCAGATGCTATACTTTTAGTCGCTG 58.791 40.000 0.00 0.00 0.00 5.18
1717 1787 5.403766 CAGATGCTATACTTTTAGTCGCTGG 59.596 44.000 0.00 0.00 0.00 4.85
1718 1788 4.730949 TGCTATACTTTTAGTCGCTGGT 57.269 40.909 0.00 0.00 0.00 4.00
1719 1789 5.080969 TGCTATACTTTTAGTCGCTGGTT 57.919 39.130 0.00 0.00 0.00 3.67
1720 1790 5.484715 TGCTATACTTTTAGTCGCTGGTTT 58.515 37.500 0.00 0.00 0.00 3.27
1721 1791 6.632909 TGCTATACTTTTAGTCGCTGGTTTA 58.367 36.000 0.00 0.00 0.00 2.01
1722 1792 6.532657 TGCTATACTTTTAGTCGCTGGTTTAC 59.467 38.462 0.00 0.00 0.00 2.01
1723 1793 6.532657 GCTATACTTTTAGTCGCTGGTTTACA 59.467 38.462 0.00 0.00 0.00 2.41
1724 1794 7.224167 GCTATACTTTTAGTCGCTGGTTTACAT 59.776 37.037 0.00 0.00 0.00 2.29
1725 1795 9.740239 CTATACTTTTAGTCGCTGGTTTACATA 57.260 33.333 0.00 0.00 0.00 2.29
1727 1797 7.916914 ACTTTTAGTCGCTGGTTTACATAAT 57.083 32.000 0.00 0.00 0.00 1.28
1729 1799 9.609346 ACTTTTAGTCGCTGGTTTACATAATAT 57.391 29.630 0.00 0.00 0.00 1.28
1730 1800 9.864034 CTTTTAGTCGCTGGTTTACATAATATG 57.136 33.333 0.00 0.00 0.00 1.78
1731 1801 8.951787 TTTAGTCGCTGGTTTACATAATATGT 57.048 30.769 10.98 10.98 46.92 2.29
1746 1816 7.759607 ACATAATATGTAATCCTTGGAAGCCT 58.240 34.615 3.75 0.00 42.78 4.58
1752 1822 9.965902 ATATGTAATCCTTGGAAGCCTAATTAG 57.034 33.333 5.43 5.43 0.00 1.73
1764 1834 8.639761 TGGAAGCCTAATTAGTTACTCATAGTC 58.360 37.037 11.50 1.17 0.00 2.59
1788 1858 5.250235 ACACTGATACATGTCTTCGGTAG 57.750 43.478 18.03 15.14 0.00 3.18
1805 1875 4.925054 TCGGTAGAACACTTATTTGGTTCG 59.075 41.667 0.00 0.00 44.20 3.95
1819 1889 3.126879 TTCGCTGCGGCTGGATTG 61.127 61.111 23.03 0.00 36.09 2.67
1822 1892 2.180017 GCTGCGGCTGGATTGTTG 59.820 61.111 11.21 0.00 35.22 3.33
1825 1895 0.957395 CTGCGGCTGGATTGTTGACT 60.957 55.000 0.00 0.00 0.00 3.41
1848 1918 8.868522 ACTTAGATCTTTTCATTGATGTTGGA 57.131 30.769 0.00 0.00 0.00 3.53
1853 1923 9.032624 AGATCTTTTCATTGATGTTGGATTTCT 57.967 29.630 0.00 0.00 0.00 2.52
1860 1930 6.494491 TCATTGATGTTGGATTTCTGTTTCCT 59.506 34.615 0.00 0.00 32.95 3.36
1893 1963 3.702045 AGTCTGATCGACCTCCCTAAAAG 59.298 47.826 12.17 0.00 43.91 2.27
1896 1966 4.775780 TCTGATCGACCTCCCTAAAAGAAA 59.224 41.667 0.00 0.00 0.00 2.52
1897 1967 5.425539 TCTGATCGACCTCCCTAAAAGAAAT 59.574 40.000 0.00 0.00 0.00 2.17
1898 1968 5.671493 TGATCGACCTCCCTAAAAGAAATC 58.329 41.667 0.00 0.00 0.00 2.17
1902 1982 4.564821 CGACCTCCCTAAAAGAAATCACCA 60.565 45.833 0.00 0.00 0.00 4.17
1903 1983 4.663334 ACCTCCCTAAAAGAAATCACCAC 58.337 43.478 0.00 0.00 0.00 4.16
1917 1997 4.613925 ATCACCACTATGCTCCTATGTG 57.386 45.455 0.00 0.00 0.00 3.21
1926 2006 1.339055 TGCTCCTATGTGTGTCCAAGC 60.339 52.381 0.00 0.00 0.00 4.01
1932 2012 1.159285 ATGTGTGTCCAAGCGATGTG 58.841 50.000 0.00 0.00 0.00 3.21
1935 2015 0.943673 TGTGTCCAAGCGATGTGTTG 59.056 50.000 0.00 0.00 0.00 3.33
1936 2016 0.385974 GTGTCCAAGCGATGTGTTGC 60.386 55.000 0.00 0.00 34.77 4.17
1986 2066 8.414629 AAAATGCTCTGTCTTCTTTTAGGAAT 57.585 30.769 0.00 0.00 0.00 3.01
1988 2068 6.808008 TGCTCTGTCTTCTTTTAGGAATTG 57.192 37.500 0.00 0.00 0.00 2.32
1993 2073 7.287061 TCTGTCTTCTTTTAGGAATTGGTTGA 58.713 34.615 0.00 0.00 0.00 3.18
1994 2074 7.777910 TCTGTCTTCTTTTAGGAATTGGTTGAA 59.222 33.333 0.00 0.00 0.00 2.69
2020 2100 1.255882 TTTGGACCATGCAATTCGCT 58.744 45.000 0.00 0.00 43.06 4.93
2042 2122 7.710907 TCGCTTCAAACTATTATTGATACTGCT 59.289 33.333 0.00 0.00 36.72 4.24
2128 2208 0.187361 TCTTTGAGGGGTGGTTTGGG 59.813 55.000 0.00 0.00 0.00 4.12
2137 2217 0.608130 GGTGGTTTGGGCCTCATTTC 59.392 55.000 4.53 0.00 0.00 2.17
2260 2340 6.765915 AAGAGGTCCATTTTGCTATTTCTC 57.234 37.500 0.00 0.00 0.00 2.87
2301 2381 4.546829 TTACTAACGGAGCATCTTTGGT 57.453 40.909 0.00 0.00 35.95 3.67
2341 2421 1.347050 ACATCTGCTCTGTCAGTTGCT 59.653 47.619 16.88 0.78 37.32 3.91
2441 2521 5.606348 ACTCTTCCCTGAGATACATGAAC 57.394 43.478 0.00 0.00 37.50 3.18
2494 2574 1.066143 CCGGTTCTTGTCACTGCCTAT 60.066 52.381 0.00 0.00 0.00 2.57
2526 2606 4.706842 ACAATGGTGTGTCTCCTACTTT 57.293 40.909 0.00 0.00 36.31 2.66
2539 2619 8.092687 GTGTCTCCTACTTTATACTTGGTTTGA 58.907 37.037 0.00 0.00 0.00 2.69
2549 2629 8.856153 TTTATACTTGGTTTGATCTTGCTGTA 57.144 30.769 0.00 0.00 0.00 2.74
2579 2659 7.840342 TTTCTCTGAGATCTAAAACATCTGC 57.160 36.000 8.42 0.00 30.30 4.26
2659 2739 1.888512 AGCCAATTGTGCGAACTTCAT 59.111 42.857 4.43 0.00 0.00 2.57
2709 2789 6.949578 GCAACAAGCTTCTTTGCATATTTA 57.050 33.333 26.74 0.00 44.17 1.40
2715 2795 8.239998 ACAAGCTTCTTTGCATATTTACTCTTC 58.760 33.333 0.00 0.00 34.99 2.87
2745 2825 2.780094 CCTCTCCGATGTGCTCGCT 61.780 63.158 0.00 0.00 46.25 4.93
2757 2837 3.664107 TGTGCTCGCTAATTTTGACTCT 58.336 40.909 0.00 0.00 0.00 3.24
2829 2909 3.744942 GCTATGTAGTCCATGTCATGCTG 59.255 47.826 7.35 0.00 34.86 4.41
2832 2912 2.093500 TGTAGTCCATGTCATGCTGGTC 60.093 50.000 7.35 0.00 34.03 4.02
2946 3026 3.632604 TCATTATCACCGTCTCACTCCTC 59.367 47.826 0.00 0.00 0.00 3.71
2948 3028 1.658686 ATCACCGTCTCACTCCTCGC 61.659 60.000 0.00 0.00 0.00 5.03
3006 3086 2.171635 GGATGCGTTCCAGTTCACC 58.828 57.895 0.77 0.00 44.74 4.02
3060 3140 4.711399 TCTTTCCTGCCATGATCATACTG 58.289 43.478 8.15 7.70 0.00 2.74
3084 3164 5.316167 AGGTAATCAGCATTCTGTTTGTGA 58.684 37.500 0.00 0.00 41.10 3.58
3085 3165 5.948162 AGGTAATCAGCATTCTGTTTGTGAT 59.052 36.000 0.00 0.00 41.10 3.06
3086 3166 6.032094 GGTAATCAGCATTCTGTTTGTGATG 58.968 40.000 0.00 0.00 41.10 3.07
3091 3171 2.727798 GCATTCTGTTTGTGATGTGTGC 59.272 45.455 0.00 0.00 0.00 4.57
3104 3185 1.285641 GTGTGCCCCGATGTTTGTG 59.714 57.895 0.00 0.00 0.00 3.33
3108 3189 1.906333 GCCCCGATGTTTGTGGGTT 60.906 57.895 0.00 0.00 41.63 4.11
3134 3215 7.942990 TCCTTTTGGTTTACGTGTTCAATAAT 58.057 30.769 0.00 0.00 41.38 1.28
3466 3631 4.858935 TGTTTGCTGCATTTGTCTAGTTC 58.141 39.130 1.84 0.00 0.00 3.01
3572 3737 9.214957 CAAGATTTTTATTTACTTTTGGGGGTC 57.785 33.333 0.00 0.00 0.00 4.46
3592 3757 5.179368 GGGTCATGTACATGTTCATATTCGG 59.821 44.000 30.03 5.69 39.72 4.30
3605 3770 8.279970 TGTTCATATTCGGTCATCTTGAAATT 57.720 30.769 0.00 0.00 0.00 1.82
3626 3791 7.941795 AATTGATGTTTGAGAAAGCTCTTTG 57.058 32.000 0.00 0.00 41.84 2.77
3640 3805 5.306532 AGCTCTTTGTATGCAATGAACTG 57.693 39.130 12.43 4.44 38.00 3.16
3709 3884 1.578583 CACCGACGTTTTTCTCACCT 58.421 50.000 0.00 0.00 0.00 4.00
3819 4029 4.524802 TCTACGGTCCCATTAGGTAGAA 57.475 45.455 0.94 0.00 37.30 2.10
3877 4088 7.381948 TCATGTTTTGAAAATGTGACATGTAGC 59.618 33.333 15.31 0.00 42.83 3.58
3881 4092 3.188254 TGAAAATGTGACATGTAGCGTGG 59.812 43.478 0.00 0.00 0.00 4.94
3975 4187 7.285566 ACATAGTCTGAATTGTGCAATCCTAT 58.714 34.615 0.00 0.00 0.00 2.57
4101 4435 4.490743 ACCGCACAATTAAAATAGGTTGC 58.509 39.130 0.00 0.00 0.00 4.17
4196 4530 5.358160 GTGGCCTCTAAATAGCAATTCTGTT 59.642 40.000 3.32 0.00 0.00 3.16
4197 4531 5.357878 TGGCCTCTAAATAGCAATTCTGTTG 59.642 40.000 3.32 0.00 0.00 3.33
4229 4563 2.452600 AGGTCTCCTTTGGTTTGCAA 57.547 45.000 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.186198 GCTTCCTCTTACTTGCCTGATTAA 58.814 41.667 0.00 0.00 0.00 1.40
35 36 3.073062 TCTTTGCTTCCTCTTACTTGCCT 59.927 43.478 0.00 0.00 0.00 4.75
223 224 1.270625 CCGGCGGCCTTCTTATATTGA 60.271 52.381 15.42 0.00 0.00 2.57
225 226 0.036306 CCCGGCGGCCTTCTTATATT 59.964 55.000 23.20 0.00 0.00 1.28
293 294 2.568623 AATCGGCAGAAGACTTTGGT 57.431 45.000 0.00 0.00 0.00 3.67
330 334 1.938861 CCAACAACCCGAACACGAG 59.061 57.895 0.00 0.00 0.00 4.18
467 471 3.131709 ACCAACCAGATCAGACAACTG 57.868 47.619 0.00 0.00 44.66 3.16
492 496 2.158608 CCAAGACAAACTTCTCCAGGGT 60.159 50.000 0.00 0.00 36.61 4.34
521 525 5.800438 GCAACGTCTAAATCTTGGAATTTCC 59.200 40.000 8.59 8.59 36.96 3.13
603 611 0.973632 TCCGGCAGTAGAACACATGT 59.026 50.000 0.00 0.00 0.00 3.21
632 640 4.606961 ACCACATAAAGCAACAAACTTCG 58.393 39.130 0.00 0.00 0.00 3.79
640 648 4.443063 GGAAACGAAACCACATAAAGCAAC 59.557 41.667 0.00 0.00 0.00 4.17
666 674 3.953612 ACAAAGTCTGGCTTGATGACAAA 59.046 39.130 0.00 0.00 37.52 2.83
699 708 7.227910 ACAACTAACTATTTGACCGACACATTT 59.772 33.333 0.00 0.00 0.00 2.32
702 711 5.603596 ACAACTAACTATTTGACCGACACA 58.396 37.500 0.00 0.00 0.00 3.72
859 870 5.652452 CCTTAAATCTGAATTCCCGTCCTTT 59.348 40.000 2.27 0.00 0.00 3.11
932 968 5.752036 AGGACAAGAGACAGATTTCATCA 57.248 39.130 0.00 0.00 0.00 3.07
947 983 6.420604 ACGTGCAAATTTTCAATTAGGACAAG 59.579 34.615 0.00 0.00 0.00 3.16
971 1007 5.850614 TCAAGTACTTTCAACCTCCTGTAC 58.149 41.667 5.07 0.00 0.00 2.90
1051 1087 1.142748 GCGTGGTCTCATCCCTCTG 59.857 63.158 0.00 0.00 0.00 3.35
1323 1359 2.862541 TGACCAAAAGAGTCACCCATG 58.137 47.619 0.00 0.00 39.29 3.66
1359 1395 0.109153 TGACCACAGATGCTTGCAGT 59.891 50.000 0.87 0.00 0.00 4.40
1387 1423 5.236263 TCATGTATACAATCATGACGCCAAC 59.764 40.000 10.14 0.00 43.29 3.77
1506 1573 7.790027 TGGGTTCCATTTTATGTAAATCATGG 58.210 34.615 8.80 8.80 35.98 3.66
1507 1574 9.263538 CATGGGTTCCATTTTATGTAAATCATG 57.736 33.333 0.00 0.00 42.23 3.07
1508 1575 8.431222 CCATGGGTTCCATTTTATGTAAATCAT 58.569 33.333 2.85 0.00 42.23 2.45
1512 1579 7.798710 TTCCATGGGTTCCATTTTATGTAAA 57.201 32.000 13.02 0.00 42.23 2.01
1515 1582 5.784906 AGTTTCCATGGGTTCCATTTTATGT 59.215 36.000 13.02 0.00 42.23 2.29
1521 1588 5.010708 ACTTAGTTTCCATGGGTTCCATT 57.989 39.130 13.02 0.00 42.23 3.16
1528 1595 9.462606 AAGAAGTTATTACTTAGTTTCCATGGG 57.537 33.333 13.02 0.00 44.51 4.00
1566 1636 8.773645 CCGAAAAATGTATCAGCATTCACTATA 58.226 33.333 0.00 0.00 38.03 1.31
1567 1637 7.283127 ACCGAAAAATGTATCAGCATTCACTAT 59.717 33.333 0.00 0.00 38.03 2.12
1568 1638 6.597672 ACCGAAAAATGTATCAGCATTCACTA 59.402 34.615 0.00 0.00 38.03 2.74
1569 1639 5.415701 ACCGAAAAATGTATCAGCATTCACT 59.584 36.000 0.00 0.00 38.03 3.41
1570 1640 5.512788 CACCGAAAAATGTATCAGCATTCAC 59.487 40.000 0.00 0.00 38.03 3.18
1571 1641 5.414144 TCACCGAAAAATGTATCAGCATTCA 59.586 36.000 0.00 0.00 38.03 2.57
1572 1642 5.879237 TCACCGAAAAATGTATCAGCATTC 58.121 37.500 0.00 0.00 38.03 2.67
1573 1643 5.895636 TCACCGAAAAATGTATCAGCATT 57.104 34.783 0.00 0.00 40.43 3.56
1574 1644 5.895636 TTCACCGAAAAATGTATCAGCAT 57.104 34.783 0.00 0.00 0.00 3.79
1575 1645 5.895636 ATTCACCGAAAAATGTATCAGCA 57.104 34.783 0.00 0.00 0.00 4.41
1576 1646 8.128582 TGATAATTCACCGAAAAATGTATCAGC 58.871 33.333 0.00 0.00 0.00 4.26
1579 1649 9.318041 CGATGATAATTCACCGAAAAATGTATC 57.682 33.333 0.00 0.00 41.74 2.24
1580 1650 8.289618 CCGATGATAATTCACCGAAAAATGTAT 58.710 33.333 0.00 0.00 41.74 2.29
1581 1651 7.281324 ACCGATGATAATTCACCGAAAAATGTA 59.719 33.333 0.00 0.00 41.74 2.29
1582 1652 6.094881 ACCGATGATAATTCACCGAAAAATGT 59.905 34.615 0.00 0.00 41.74 2.71
1583 1653 6.494842 ACCGATGATAATTCACCGAAAAATG 58.505 36.000 0.00 0.00 41.74 2.32
1584 1654 6.693315 ACCGATGATAATTCACCGAAAAAT 57.307 33.333 0.00 0.00 41.74 1.82
1585 1655 7.635423 CATACCGATGATAATTCACCGAAAAA 58.365 34.615 0.00 0.00 41.74 1.94
1586 1656 6.293190 GCATACCGATGATAATTCACCGAAAA 60.293 38.462 0.00 0.00 41.74 2.29
1587 1657 5.178623 GCATACCGATGATAATTCACCGAAA 59.821 40.000 0.00 0.00 41.74 3.46
1588 1658 4.688879 GCATACCGATGATAATTCACCGAA 59.311 41.667 0.00 0.00 41.74 4.30
1589 1659 4.242475 GCATACCGATGATAATTCACCGA 58.758 43.478 0.00 0.00 41.74 4.69
1590 1660 3.370978 GGCATACCGATGATAATTCACCG 59.629 47.826 0.00 0.00 38.70 4.94
1591 1661 4.393062 CAGGCATACCGATGATAATTCACC 59.607 45.833 0.00 0.00 42.76 4.02
1592 1662 4.997395 ACAGGCATACCGATGATAATTCAC 59.003 41.667 0.00 0.00 42.76 3.18
1593 1663 4.996758 CACAGGCATACCGATGATAATTCA 59.003 41.667 0.00 0.00 42.76 2.57
1594 1664 5.120830 GTCACAGGCATACCGATGATAATTC 59.879 44.000 0.00 0.00 42.76 2.17
1595 1665 4.997395 GTCACAGGCATACCGATGATAATT 59.003 41.667 0.00 0.00 42.76 1.40
1596 1666 4.040339 TGTCACAGGCATACCGATGATAAT 59.960 41.667 0.00 0.00 42.76 1.28
1597 1667 3.386402 TGTCACAGGCATACCGATGATAA 59.614 43.478 0.00 0.00 42.76 1.75
1598 1668 2.962421 TGTCACAGGCATACCGATGATA 59.038 45.455 0.00 0.00 42.76 2.15
1599 1669 1.762370 TGTCACAGGCATACCGATGAT 59.238 47.619 0.00 0.00 42.76 2.45
1600 1670 1.134818 GTGTCACAGGCATACCGATGA 60.135 52.381 0.00 0.00 42.76 2.92
1601 1671 1.290203 GTGTCACAGGCATACCGATG 58.710 55.000 0.00 0.00 42.76 3.84
1602 1672 0.179111 CGTGTCACAGGCATACCGAT 60.179 55.000 3.42 0.00 42.76 4.18
1603 1673 1.214325 CGTGTCACAGGCATACCGA 59.786 57.895 3.42 0.00 42.76 4.69
1604 1674 1.076533 GTCGTGTCACAGGCATACCG 61.077 60.000 3.42 0.00 42.76 4.02
1605 1675 0.739813 GGTCGTGTCACAGGCATACC 60.740 60.000 3.42 0.00 0.00 2.73
1606 1676 0.739813 GGGTCGTGTCACAGGCATAC 60.740 60.000 3.42 0.00 0.00 2.39
1607 1677 0.902984 AGGGTCGTGTCACAGGCATA 60.903 55.000 3.42 0.00 0.00 3.14
1608 1678 1.768684 AAGGGTCGTGTCACAGGCAT 61.769 55.000 3.42 0.00 0.00 4.40
1609 1679 2.377628 GAAGGGTCGTGTCACAGGCA 62.378 60.000 3.42 0.00 0.00 4.75
1610 1680 1.668151 GAAGGGTCGTGTCACAGGC 60.668 63.158 3.42 0.00 0.00 4.85
1611 1681 0.038159 GAGAAGGGTCGTGTCACAGG 60.038 60.000 3.42 0.00 0.00 4.00
1612 1682 0.962489 AGAGAAGGGTCGTGTCACAG 59.038 55.000 3.42 0.00 0.00 3.66
1613 1683 0.673985 CAGAGAAGGGTCGTGTCACA 59.326 55.000 3.42 0.00 0.00 3.58
1614 1684 0.674534 ACAGAGAAGGGTCGTGTCAC 59.325 55.000 0.00 0.00 0.00 3.67
1615 1685 0.959553 GACAGAGAAGGGTCGTGTCA 59.040 55.000 0.00 0.00 40.07 3.58
1616 1686 0.959553 TGACAGAGAAGGGTCGTGTC 59.040 55.000 0.00 0.00 40.43 3.67
1617 1687 1.273606 CATGACAGAGAAGGGTCGTGT 59.726 52.381 0.00 0.00 43.00 4.49
1618 1688 2.001812 CATGACAGAGAAGGGTCGTG 57.998 55.000 0.00 0.00 42.57 4.35
1619 1689 0.247736 GCATGACAGAGAAGGGTCGT 59.752 55.000 0.00 0.00 36.83 4.34
1620 1690 0.460987 GGCATGACAGAGAAGGGTCG 60.461 60.000 0.00 0.00 36.83 4.79
1621 1691 0.908198 AGGCATGACAGAGAAGGGTC 59.092 55.000 0.00 0.00 34.63 4.46
1622 1692 1.834263 GTAGGCATGACAGAGAAGGGT 59.166 52.381 0.00 0.00 0.00 4.34
1623 1693 2.114616 AGTAGGCATGACAGAGAAGGG 58.885 52.381 0.00 0.00 0.00 3.95
1624 1694 3.902881 AAGTAGGCATGACAGAGAAGG 57.097 47.619 0.00 0.00 0.00 3.46
1625 1695 4.160439 TGGTAAGTAGGCATGACAGAGAAG 59.840 45.833 0.00 0.00 0.00 2.85
1626 1696 4.093743 TGGTAAGTAGGCATGACAGAGAA 58.906 43.478 0.00 0.00 0.00 2.87
1627 1697 3.708451 TGGTAAGTAGGCATGACAGAGA 58.292 45.455 0.00 0.00 0.00 3.10
1628 1698 4.626042 GATGGTAAGTAGGCATGACAGAG 58.374 47.826 0.00 0.00 0.00 3.35
1629 1699 3.068165 CGATGGTAAGTAGGCATGACAGA 59.932 47.826 0.00 0.00 0.00 3.41
1630 1700 3.068165 TCGATGGTAAGTAGGCATGACAG 59.932 47.826 0.00 0.00 0.00 3.51
1631 1701 3.028130 TCGATGGTAAGTAGGCATGACA 58.972 45.455 0.00 0.00 0.00 3.58
1632 1702 3.318275 TCTCGATGGTAAGTAGGCATGAC 59.682 47.826 0.00 0.00 0.00 3.06
1633 1703 3.562182 TCTCGATGGTAAGTAGGCATGA 58.438 45.455 0.00 0.00 0.00 3.07
1634 1704 3.319405 ACTCTCGATGGTAAGTAGGCATG 59.681 47.826 0.00 0.00 0.00 4.06
1635 1705 3.567397 ACTCTCGATGGTAAGTAGGCAT 58.433 45.455 0.00 0.00 0.00 4.40
1636 1706 3.014304 ACTCTCGATGGTAAGTAGGCA 57.986 47.619 0.00 0.00 0.00 4.75
1637 1707 3.130693 ACAACTCTCGATGGTAAGTAGGC 59.869 47.826 0.00 0.00 0.00 3.93
1638 1708 4.985538 ACAACTCTCGATGGTAAGTAGG 57.014 45.455 0.00 0.00 0.00 3.18
1639 1709 7.481642 ACATTACAACTCTCGATGGTAAGTAG 58.518 38.462 0.00 0.00 0.00 2.57
1640 1710 7.400599 ACATTACAACTCTCGATGGTAAGTA 57.599 36.000 0.00 0.00 0.00 2.24
1641 1711 6.282199 ACATTACAACTCTCGATGGTAAGT 57.718 37.500 0.00 0.00 0.00 2.24
1642 1712 6.811665 TCAACATTACAACTCTCGATGGTAAG 59.188 38.462 0.00 0.00 0.00 2.34
1643 1713 6.693466 TCAACATTACAACTCTCGATGGTAA 58.307 36.000 0.00 0.00 0.00 2.85
1644 1714 6.275494 TCAACATTACAACTCTCGATGGTA 57.725 37.500 0.00 0.00 0.00 3.25
1645 1715 5.147330 TCAACATTACAACTCTCGATGGT 57.853 39.130 0.00 0.00 0.00 3.55
1646 1716 6.668541 ATTCAACATTACAACTCTCGATGG 57.331 37.500 0.00 0.00 0.00 3.51
1647 1717 8.210525 CGATATTCAACATTACAACTCTCGATG 58.789 37.037 0.00 0.00 0.00 3.84
1648 1718 8.135529 TCGATATTCAACATTACAACTCTCGAT 58.864 33.333 0.00 0.00 0.00 3.59
1649 1719 7.477494 TCGATATTCAACATTACAACTCTCGA 58.523 34.615 0.00 0.00 0.00 4.04
1650 1720 7.679659 TCGATATTCAACATTACAACTCTCG 57.320 36.000 0.00 0.00 0.00 4.04
1656 1726 9.891828 GCCAATTATCGATATTCAACATTACAA 57.108 29.630 5.84 0.00 0.00 2.41
1657 1727 9.283768 AGCCAATTATCGATATTCAACATTACA 57.716 29.630 5.84 0.00 0.00 2.41
1658 1728 9.546909 CAGCCAATTATCGATATTCAACATTAC 57.453 33.333 5.84 0.00 0.00 1.89
1659 1729 9.283768 ACAGCCAATTATCGATATTCAACATTA 57.716 29.630 5.84 0.00 0.00 1.90
1660 1730 8.169977 ACAGCCAATTATCGATATTCAACATT 57.830 30.769 5.84 0.00 0.00 2.71
1661 1731 7.750229 ACAGCCAATTATCGATATTCAACAT 57.250 32.000 5.84 0.00 0.00 2.71
1662 1732 8.846943 ATACAGCCAATTATCGATATTCAACA 57.153 30.769 5.84 0.00 0.00 3.33
1664 1734 9.083080 CGTATACAGCCAATTATCGATATTCAA 57.917 33.333 5.84 0.00 0.00 2.69
1665 1735 8.248253 ACGTATACAGCCAATTATCGATATTCA 58.752 33.333 5.84 0.00 0.00 2.57
1666 1736 8.630278 ACGTATACAGCCAATTATCGATATTC 57.370 34.615 5.84 0.00 0.00 1.75
1667 1737 8.997621 AACGTATACAGCCAATTATCGATATT 57.002 30.769 5.84 0.00 0.00 1.28
1668 1738 8.248253 TGAACGTATACAGCCAATTATCGATAT 58.752 33.333 5.84 0.00 0.00 1.63
1669 1739 7.595604 TGAACGTATACAGCCAATTATCGATA 58.404 34.615 0.00 0.00 0.00 2.92
1670 1740 6.452242 TGAACGTATACAGCCAATTATCGAT 58.548 36.000 2.16 2.16 0.00 3.59
1671 1741 5.834169 TGAACGTATACAGCCAATTATCGA 58.166 37.500 3.32 0.00 0.00 3.59
1672 1742 5.918576 TCTGAACGTATACAGCCAATTATCG 59.081 40.000 3.32 0.00 34.57 2.92
1673 1743 7.622256 GCATCTGAACGTATACAGCCAATTATC 60.622 40.741 3.32 0.00 34.57 1.75
1674 1744 6.147821 GCATCTGAACGTATACAGCCAATTAT 59.852 38.462 3.32 0.00 34.57 1.28
1675 1745 5.465390 GCATCTGAACGTATACAGCCAATTA 59.535 40.000 3.32 0.00 34.57 1.40
1676 1746 4.273480 GCATCTGAACGTATACAGCCAATT 59.727 41.667 3.32 0.00 34.57 2.32
1677 1747 3.809832 GCATCTGAACGTATACAGCCAAT 59.190 43.478 3.32 0.55 34.57 3.16
1678 1748 3.118775 AGCATCTGAACGTATACAGCCAA 60.119 43.478 3.32 0.00 34.57 4.52
1679 1749 2.430694 AGCATCTGAACGTATACAGCCA 59.569 45.455 3.32 0.00 34.57 4.75
1680 1750 3.099267 AGCATCTGAACGTATACAGCC 57.901 47.619 3.32 0.00 34.57 4.85
1681 1751 6.613233 AGTATAGCATCTGAACGTATACAGC 58.387 40.000 3.32 2.47 34.57 4.40
1682 1752 9.464714 AAAAGTATAGCATCTGAACGTATACAG 57.535 33.333 3.32 9.90 31.62 2.74
1686 1756 9.680315 GACTAAAAGTATAGCATCTGAACGTAT 57.320 33.333 0.00 0.00 0.00 3.06
1687 1757 7.854422 CGACTAAAAGTATAGCATCTGAACGTA 59.146 37.037 0.00 0.00 0.00 3.57
1688 1758 6.691818 CGACTAAAAGTATAGCATCTGAACGT 59.308 38.462 0.00 0.00 0.00 3.99
1689 1759 6.345093 GCGACTAAAAGTATAGCATCTGAACG 60.345 42.308 0.00 0.00 0.00 3.95
1690 1760 6.697892 AGCGACTAAAAGTATAGCATCTGAAC 59.302 38.462 0.00 0.00 0.00 3.18
1691 1761 6.697455 CAGCGACTAAAAGTATAGCATCTGAA 59.303 38.462 0.00 0.00 0.00 3.02
1692 1762 6.209361 CAGCGACTAAAAGTATAGCATCTGA 58.791 40.000 0.00 0.00 0.00 3.27
1693 1763 5.403766 CCAGCGACTAAAAGTATAGCATCTG 59.596 44.000 0.00 0.00 0.00 2.90
1694 1764 5.069251 ACCAGCGACTAAAAGTATAGCATCT 59.931 40.000 0.00 0.00 0.00 2.90
1695 1765 5.290386 ACCAGCGACTAAAAGTATAGCATC 58.710 41.667 0.00 0.00 0.00 3.91
1696 1766 5.277857 ACCAGCGACTAAAAGTATAGCAT 57.722 39.130 0.00 0.00 0.00 3.79
1697 1767 4.730949 ACCAGCGACTAAAAGTATAGCA 57.269 40.909 0.00 0.00 0.00 3.49
1698 1768 6.532657 TGTAAACCAGCGACTAAAAGTATAGC 59.467 38.462 0.00 0.00 0.00 2.97
1699 1769 8.644318 ATGTAAACCAGCGACTAAAAGTATAG 57.356 34.615 0.00 0.00 0.00 1.31
1701 1771 9.609346 ATTATGTAAACCAGCGACTAAAAGTAT 57.391 29.630 0.00 0.00 0.00 2.12
1703 1773 7.916914 ATTATGTAAACCAGCGACTAAAAGT 57.083 32.000 0.00 0.00 0.00 2.66
1704 1774 9.864034 CATATTATGTAAACCAGCGACTAAAAG 57.136 33.333 0.00 0.00 0.00 2.27
1705 1775 9.386010 ACATATTATGTAAACCAGCGACTAAAA 57.614 29.630 7.55 0.00 42.78 1.52
1706 1776 8.951787 ACATATTATGTAAACCAGCGACTAAA 57.048 30.769 7.55 0.00 42.78 1.85
1720 1790 8.890472 AGGCTTCCAAGGATTACATATTATGTA 58.110 33.333 11.64 11.64 44.38 2.29
1721 1791 7.759607 AGGCTTCCAAGGATTACATATTATGT 58.240 34.615 13.57 13.57 46.92 2.29
1722 1792 9.739276 TTAGGCTTCCAAGGATTACATATTATG 57.261 33.333 0.00 2.03 0.00 1.90
1726 1796 9.965902 CTAATTAGGCTTCCAAGGATTACATAT 57.034 33.333 4.42 0.00 0.00 1.78
1727 1797 8.945193 ACTAATTAGGCTTCCAAGGATTACATA 58.055 33.333 16.73 0.00 0.00 2.29
1728 1798 7.816411 ACTAATTAGGCTTCCAAGGATTACAT 58.184 34.615 16.73 0.00 0.00 2.29
1729 1799 7.208064 ACTAATTAGGCTTCCAAGGATTACA 57.792 36.000 16.73 0.00 0.00 2.41
1730 1800 9.053840 GTAACTAATTAGGCTTCCAAGGATTAC 57.946 37.037 16.73 7.66 0.00 1.89
1731 1801 8.999895 AGTAACTAATTAGGCTTCCAAGGATTA 58.000 33.333 16.73 0.00 0.00 1.75
1732 1802 7.873195 AGTAACTAATTAGGCTTCCAAGGATT 58.127 34.615 16.73 0.45 0.00 3.01
1733 1803 7.127339 TGAGTAACTAATTAGGCTTCCAAGGAT 59.873 37.037 16.73 0.00 0.00 3.24
1734 1804 6.442564 TGAGTAACTAATTAGGCTTCCAAGGA 59.557 38.462 16.73 0.00 0.00 3.36
1735 1805 6.650120 TGAGTAACTAATTAGGCTTCCAAGG 58.350 40.000 16.73 0.00 0.00 3.61
1736 1806 9.482627 CTATGAGTAACTAATTAGGCTTCCAAG 57.517 37.037 16.73 2.15 0.00 3.61
1737 1807 8.989131 ACTATGAGTAACTAATTAGGCTTCCAA 58.011 33.333 16.73 0.00 0.00 3.53
1738 1808 8.548880 ACTATGAGTAACTAATTAGGCTTCCA 57.451 34.615 16.73 8.97 0.00 3.53
1739 1809 8.639761 TGACTATGAGTAACTAATTAGGCTTCC 58.360 37.037 16.73 3.95 0.00 3.46
1741 1811 9.819267 GTTGACTATGAGTAACTAATTAGGCTT 57.181 33.333 16.73 5.62 0.00 4.35
1742 1812 8.978472 TGTTGACTATGAGTAACTAATTAGGCT 58.022 33.333 16.73 10.96 0.00 4.58
1743 1813 9.032420 GTGTTGACTATGAGTAACTAATTAGGC 57.968 37.037 16.73 6.64 0.00 3.93
1752 1822 9.025020 CATGTATCAGTGTTGACTATGAGTAAC 57.975 37.037 0.00 0.00 35.83 2.50
1764 1834 4.245660 ACCGAAGACATGTATCAGTGTTG 58.754 43.478 0.00 0.00 0.00 3.33
1788 1858 3.234386 GCAGCGAACCAAATAAGTGTTC 58.766 45.455 0.00 0.00 36.02 3.18
1805 1875 2.180017 CAACAATCCAGCCGCAGC 59.820 61.111 0.00 0.00 40.32 5.25
1822 1892 8.950210 TCCAACATCAATGAAAAGATCTAAGTC 58.050 33.333 0.00 0.00 0.00 3.01
1893 1963 5.468072 CACATAGGAGCATAGTGGTGATTTC 59.532 44.000 0.00 0.00 0.00 2.17
1896 1966 3.969976 ACACATAGGAGCATAGTGGTGAT 59.030 43.478 0.00 0.00 34.65 3.06
1897 1967 3.132824 CACACATAGGAGCATAGTGGTGA 59.867 47.826 0.00 0.00 34.65 4.02
1898 1968 3.118629 ACACACATAGGAGCATAGTGGTG 60.119 47.826 0.00 0.00 34.65 4.17
1902 1982 3.374764 TGGACACACATAGGAGCATAGT 58.625 45.455 0.00 0.00 0.00 2.12
1903 1983 4.375272 CTTGGACACACATAGGAGCATAG 58.625 47.826 0.00 0.00 0.00 2.23
1917 1997 0.385974 GCAACACATCGCTTGGACAC 60.386 55.000 0.00 0.00 0.00 3.67
1926 2006 1.580437 TGTGCCATGCAACACATCG 59.420 52.632 14.43 0.00 41.67 3.84
1932 2012 2.282701 ATTTCGATGTGCCATGCAAC 57.717 45.000 0.00 0.00 41.47 4.17
1935 2015 3.365832 CACTTATTTCGATGTGCCATGC 58.634 45.455 0.00 0.00 0.00 4.06
1936 2016 3.365832 GCACTTATTTCGATGTGCCATG 58.634 45.455 13.30 0.00 46.84 3.66
1963 2043 7.094032 CCAATTCCTAAAAGAAGACAGAGCATT 60.094 37.037 0.00 0.00 0.00 3.56
1971 2051 8.029522 GGATTCAACCAATTCCTAAAAGAAGAC 58.970 37.037 0.00 0.00 0.00 3.01
1986 2066 5.398236 TGGTCCAAATAAGGATTCAACCAA 58.602 37.500 0.00 0.00 40.42 3.67
1988 2068 5.682212 GCATGGTCCAAATAAGGATTCAACC 60.682 44.000 0.00 0.00 40.42 3.77
1993 2073 6.564557 AATTGCATGGTCCAAATAAGGATT 57.435 33.333 0.00 0.00 40.42 3.01
1994 2074 5.221303 CGAATTGCATGGTCCAAATAAGGAT 60.221 40.000 0.00 0.00 40.42 3.24
2056 2136 2.158519 TCCCGATAGCACATCACCTAGA 60.159 50.000 0.00 0.00 0.00 2.43
2058 2138 2.364324 GTTCCCGATAGCACATCACCTA 59.636 50.000 0.00 0.00 0.00 3.08
2128 2208 3.274288 ACGAGAATTCCAGAAATGAGGC 58.726 45.455 0.65 0.00 0.00 4.70
2301 2381 5.009854 TGTGTATCTCAATGAATCTGCGA 57.990 39.130 0.00 0.00 0.00 5.10
2341 2421 3.256879 TGACAACAAAAACCACAGCAAGA 59.743 39.130 0.00 0.00 0.00 3.02
2494 2574 4.402829 ACACACCATTGTAGTGGCAAATA 58.597 39.130 9.59 0.00 43.27 1.40
2526 2606 7.620880 ACTACAGCAAGATCAAACCAAGTATA 58.379 34.615 0.00 0.00 0.00 1.47
2539 2619 6.705302 TCAGAGAAATGAACTACAGCAAGAT 58.295 36.000 0.00 0.00 0.00 2.40
2549 2629 9.956640 ATGTTTTAGATCTCAGAGAAATGAACT 57.043 29.630 3.63 0.92 0.00 3.01
2579 2659 6.075762 TGTGAACTGTCCAATCATGAAAAG 57.924 37.500 0.00 0.00 0.00 2.27
2616 2696 6.096282 GCTTAGTCTGACTTCTATCTTCCAGT 59.904 42.308 16.53 0.00 0.00 4.00
2659 2739 3.281727 AACACTTGAACAGAGAGCCAA 57.718 42.857 0.00 0.00 0.00 4.52
2707 2787 1.098050 GTACCCTCGCCGAAGAGTAA 58.902 55.000 6.41 0.00 36.56 2.24
2709 2789 2.050934 GGTACCCTCGCCGAAGAGT 61.051 63.158 0.00 0.00 36.56 3.24
2745 2825 9.396022 GGAATATGAAGGTCAGAGTCAAAATTA 57.604 33.333 3.20 0.00 34.77 1.40
2757 2837 5.131642 AGAGCTGAATGGAATATGAAGGTCA 59.868 40.000 0.00 0.00 34.11 4.02
2829 2909 5.361427 GCAAAGAAGACTATAGGGAAGACC 58.639 45.833 4.43 0.00 40.67 3.85
2832 2912 4.410555 AGGGCAAAGAAGACTATAGGGAAG 59.589 45.833 4.43 0.00 0.00 3.46
2924 3004 3.632333 AGGAGTGAGACGGTGATAATGA 58.368 45.455 0.00 0.00 0.00 2.57
2946 3026 2.540361 GGCAGCAAGATAAATCACAGCG 60.540 50.000 0.00 0.00 0.00 5.18
2948 3028 4.157289 AGTTGGCAGCAAGATAAATCACAG 59.843 41.667 3.63 0.00 0.00 3.66
3006 3086 2.047844 ACAGCAGCTGTAGCACCG 60.048 61.111 27.22 0.00 43.46 4.94
3060 3140 5.412594 TCACAAACAGAATGCTGATTACCTC 59.587 40.000 8.02 0.00 45.17 3.85
3084 3164 0.539438 ACAAACATCGGGGCACACAT 60.539 50.000 0.00 0.00 0.00 3.21
3085 3165 1.152860 ACAAACATCGGGGCACACA 60.153 52.632 0.00 0.00 0.00 3.72
3086 3166 1.285641 CACAAACATCGGGGCACAC 59.714 57.895 0.00 0.00 0.00 3.82
3091 3171 0.601057 GAAACCCACAAACATCGGGG 59.399 55.000 0.00 0.00 44.96 5.73
3104 3185 3.130869 ACACGTAAACCAAAAGGAAACCC 59.869 43.478 0.00 0.00 0.00 4.11
3108 3189 5.640189 TTGAACACGTAAACCAAAAGGAA 57.360 34.783 0.00 0.00 0.00 3.36
3134 3215 8.084073 CCTGAAGAAACAATGAGCAGAATAAAA 58.916 33.333 0.00 0.00 0.00 1.52
3466 3631 2.614057 GAGCCGGATTACATGTTCAAGG 59.386 50.000 5.05 5.36 0.00 3.61
3562 3727 3.534357 ACATGTACATGACCCCCAAAA 57.466 42.857 36.36 0.00 41.20 2.44
3566 3731 2.799126 TGAACATGTACATGACCCCC 57.201 50.000 36.36 20.84 41.20 5.40
3572 3737 6.843069 TGACCGAATATGAACATGTACATG 57.157 37.500 29.97 29.97 44.15 3.21
3592 3757 9.467258 TTTCTCAAACATCAATTTCAAGATGAC 57.533 29.630 9.74 0.00 43.28 3.06
3605 3770 7.587629 CATACAAAGAGCTTTCTCAAACATCA 58.412 34.615 0.00 0.00 41.81 3.07
3626 3791 7.934457 AGAATATGGTTCAGTTCATTGCATAC 58.066 34.615 0.00 0.00 0.00 2.39
3640 3805 4.232091 TGTCTCCCCCTAGAATATGGTTC 58.768 47.826 0.00 0.00 0.00 3.62
3709 3884 1.819288 TCGGTGTTTGCCTTTTTCACA 59.181 42.857 0.00 0.00 0.00 3.58
3721 3896 2.719354 GTTTGCGGCTCGGTGTTT 59.281 55.556 0.00 0.00 0.00 2.83
3726 3936 2.511600 CCTAGGTTTGCGGCTCGG 60.512 66.667 0.00 0.00 0.00 4.63
3761 3971 0.249868 TGTGGCCACAAGAGAAGACG 60.250 55.000 36.10 0.00 38.56 4.18
3850 4061 9.247126 CTACATGTCACATTTTCAAAACATGAA 57.753 29.630 15.67 2.46 46.22 2.57
3881 4092 1.062587 GACACCATTGATAGCACGCAC 59.937 52.381 0.00 0.00 0.00 5.34
3975 4187 2.739287 CGCTATGGTAAACGGTGCCTTA 60.739 50.000 0.00 0.00 32.04 2.69
4075 4409 7.309920 CAACCTATTTTAATTGTGCGGTAAGT 58.690 34.615 0.00 0.00 0.00 2.24
4078 4412 5.642686 GCAACCTATTTTAATTGTGCGGTA 58.357 37.500 0.00 0.00 0.00 4.02
4196 4530 5.416271 AGGAGACCTAAGCGTTTTTATCA 57.584 39.130 0.00 0.00 28.47 2.15
4197 4531 6.403309 CCAAAGGAGACCTAAGCGTTTTTATC 60.403 42.308 0.00 0.00 31.13 1.75


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.